Search Results for "database tool"

CBFLIB is a library of ANSI-C functions providing a simple mechanism for accessing Crystallographic Binary Files (CBF files) and Image-supporting CIF (imgCIF) files. The CBFLIB API is loosely based on the CIFPARSE API for mmCIF files.

Taxy is a tool for browsing and quering data organized as a taxonomy. Through the use of plugins it allows to connect to different data sources, such as the NCBI species taxonomy or the catalogue of biomedical services of the EU project ACGT.

Workbench for visualizing biological networks (regulatory, interaction, and metabolic). Can be used as a front-end for BNDB datawarehouses, but also as stand-alone tool.

Perl Bioinformatic Utility Tool I have development during the time I have to analysis Biology data.

AutoMATRIX is a tool to predict key transcription factors in microarray experiments.

ClinStudyWeb is designed to provide a flexible infrastructure for managing patient and assay data from clinical studies. It uses a plugin system for study-specific web forms and arbitrarily complex test classifiers, and supports XML import/export.

Information System "Supercritical Fluid Extraction" has developed as tool for collecting and analyzing the experimental data from various supercritical fluids experiments. The final target is to help to scientists who worked with supercritical fluids to predict some useful properties such as density, solubility etc. In order to calculate molecular descriptors, parse SMILES and another applied purposes is used Chemistry Development Kit (https://sourceforge.net/projects/cdk).

Pigeon is a tool for metagenomic analyses.

A simple tool to design DNA primers for mutagenesis in BGME lab (JHU). Allows users to select or enter background sequence and add current and new mutations. During the design process, users are presented with various updating checks to guide them.

Software for making Clusters of Orthologous Groups (featuring the new EdgeSearch algorithm). Latest ref: Kristensen DM, Kannan L, Coleman MK, Wolf YI, Sorokin A, Koonin EV, Mushegian A. Bioinformatics 2010.

MRS is a tool to quickly and easily store and index large flat file databanks and in a space efficient manner. It is currently used to index huge bioinformatics databanks but it is not limited to this area.

AnnTools is an efficient, fast and robust bioinformatics tool annotating SNP and CNV calls generated from sequencing and microarray data.

A simple tool to import the diff, gtf and tracking files from cufflinks, cuffcompare, cuffdiff into a new sqlite database for data mining.

Cloe (Closure Editor) is a graphical, Java based tool used for editing contigs, resolving contig features, and closing both sequencing and physical gaps.

This tool is designed to solve generalized pattern matching problem, by which we only find a set of sub-patterns, ignoring the gaps in between the sub-patterns. This tool is extremely fast and also has good tolerance to errors.

Metmask has moved to github http://github.com/hredestig/metmask Metmask is a tool written in python for managing chemical identifiers for metabolomics experiments. It can incorporate identifiers from local textfiles, several online databases, query PubChem and record all found associations in a local sqlite database.

Neurospaces is a development center for tools in computational neuroscience. See http://www.neurospaces.org/

A Java-based tool to visualize, integrate and analyze LC-MS/MS proteomics data.

A PHP webapp to upload taxonomic checklists as Excel or CSV files to be served as TDWG TCS XML/RDF. It can handle multiple checklists, has a Tapir light webservice and a taxonomic tree of species names created from taxonomy in a checklist can be browsed.

The Functional Annotation and Correlation Tool allows the meta-analysis of data from high-throughput experiments (typically microarrays) by annotating (clones, genes, GeneOntology, location, etc.) and correlating data sets to identify important patterns.

Venndiagram comparison for ProteinExperiments in the PRIDE Database

Genome Expression Pathway Analysis Tool - Analysis and Visualization of Microarray Gene Expression Data under Genomic, Proteomic and Metabolic Context

The Genomic Diversity and Phenotype Connection (GDPC) written in JAVA uses web services to make XML formatted data publicly available. The GDPC Browser (front-end GUI) can access these services, and other applications can use the API.

Evaluation of STICS simulation tool models.

Cyclone aims at facilitating the use of BioCyc, a biological pathway tool. Cyclone provides a comprehensive library of Java classes.